Starting phenix.real_space_refine on Fri Aug 22 13:00:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.map" model { file = "/net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xob_38525/08_2025/8xob_38525.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 1904 2.51 5 N 443 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2858 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2858 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.03, per 1000 atoms: 0.36 Number of scatterers: 2858 At special positions: 0 Unit cell: (56.1, 63.75, 72.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 484 8.00 N 443 7.00 C 1904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 121.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 91.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 3.941A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 130 through 157 removed outlier: 3.530A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 135 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 4.015A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.670A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 323 removed outlier: 4.110A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.785A pdb=" N LEU A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.606A pdb=" N SER A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 5.052A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 435 removed outlier: 3.810A pdb=" N ILE A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 469 240 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.47 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 855 1.34 - 1.46: 549 1.46 - 1.58: 1476 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2926 Sorted by residual: bond pdb=" N ARG A 326 " pdb=" CA ARG A 326 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.15e+00 bond pdb=" N SER A 325 " pdb=" CA SER A 325 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.34e-02 5.57e+03 6.77e+00 bond pdb=" N LYS A 327 " pdb=" CA LYS A 327 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.74e+00 bond pdb=" C PRO A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.30e-02 5.92e+03 2.91e+00 bond pdb=" CA SER A 325 " pdb=" CB SER A 325 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.61e-02 3.86e+03 2.33e+00 ... (remaining 2921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 3889 2.07 - 4.13: 70 4.13 - 6.20: 21 6.20 - 8.26: 3 8.26 - 10.33: 3 Bond angle restraints: 3986 Sorted by residual: angle pdb=" N GLY A 227 " pdb=" CA GLY A 227 " pdb=" C GLY A 227 " ideal model delta sigma weight residual 113.37 119.78 -6.41 1.34e+00 5.57e-01 2.29e+01 angle pdb=" CA ARG A 326 " pdb=" C ARG A 326 " pdb=" O ARG A 326 " ideal model delta sigma weight residual 121.94 118.07 3.87 1.15e+00 7.56e-01 1.13e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.48 -6.67 2.21e+00 2.05e-01 9.11e+00 angle pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " pdb=" CG LEU A 228 " ideal model delta sigma weight residual 116.30 126.63 -10.33 3.50e+00 8.16e-02 8.71e+00 angle pdb=" CA SER A 325 " pdb=" C SER A 325 " pdb=" O SER A 325 " ideal model delta sigma weight residual 121.87 118.50 3.37 1.16e+00 7.43e-01 8.44e+00 ... (remaining 3981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 1569 17.20 - 34.40: 126 34.40 - 51.59: 14 51.59 - 68.79: 2 68.79 - 85.99: 2 Dihedral angle restraints: 1713 sinusoidal: 618 harmonic: 1095 Sorted by residual: dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N VAL A 41 " pdb=" CA VAL A 41 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA SER A 416 " pdb=" C SER A 416 " pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 1710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 243 0.027 - 0.055: 149 0.055 - 0.082: 59 0.082 - 0.110: 22 0.110 - 0.137: 9 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA PRO A 159 " pdb=" N PRO A 159 " pdb=" C PRO A 159 " pdb=" CB PRO A 159 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 479 not shown) Planarity restraints: 490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 161 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 283 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 284 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.020 5.00e-02 4.00e+02 ... (remaining 487 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 982 2.87 - 3.37: 2949 3.37 - 3.88: 4460 3.88 - 4.39: 5049 4.39 - 4.90: 8869 Nonbonded interactions: 22309 Sorted by model distance: nonbonded pdb=" O SER A 416 " pdb=" OG SER A 416 " model vdw 2.358 3.040 nonbonded pdb=" NH2 ARG A 217 " pdb=" OD2 ASP A 411 " model vdw 2.455 3.120 nonbonded pdb=" O THR A 286 " pdb=" NZ LYS A 290 " model vdw 2.530 3.120 nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.560 3.040 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.573 2.776 ... (remaining 22304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.330 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2926 Z= 0.242 Angle : 0.805 10.330 3986 Z= 0.424 Chirality : 0.044 0.137 482 Planarity : 0.006 0.043 490 Dihedral : 12.866 85.990 1015 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.38), residues: 383 helix: -0.64 (0.26), residues: 313 sheet: None (None), residues: 0 loop : -3.01 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.013 0.001 TYR A 408 PHE 0.016 0.002 PHE A 348 TRP 0.010 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 2926) covalent geometry : angle 0.80484 ( 3986) hydrogen bonds : bond 0.13020 ( 240) hydrogen bonds : angle 5.72270 ( 714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0655 time to fit residues: 3.1942 Evaluate side-chains 32 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 146 ASN A 192 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135532 restraints weight = 3007.580| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.80 r_work: 0.3463 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2926 Z= 0.149 Angle : 0.674 10.005 3986 Z= 0.322 Chirality : 0.041 0.155 482 Planarity : 0.006 0.044 490 Dihedral : 4.559 16.863 405 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.67 % Allowed : 11.37 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.42), residues: 383 helix: 1.08 (0.29), residues: 301 sheet: None (None), residues: 0 loop : -2.09 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.010 0.001 TYR A 422 PHE 0.013 0.001 PHE A 393 TRP 0.005 0.001 TRP A 451 HIS 0.000 0.000 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2926) covalent geometry : angle 0.67377 ( 3986) hydrogen bonds : bond 0.05534 ( 240) hydrogen bonds : angle 4.57557 ( 714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.106 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.0529 time to fit residues: 2.5852 Evaluate side-chains 31 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132673 restraints weight = 3051.735| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.82 r_work: 0.3425 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2926 Z= 0.169 Angle : 0.689 10.022 3986 Z= 0.329 Chirality : 0.042 0.140 482 Planarity : 0.005 0.042 490 Dihedral : 4.488 17.255 405 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.34 % Allowed : 14.38 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.43), residues: 383 helix: 1.37 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.19 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 413 TYR 0.013 0.001 TYR A 422 PHE 0.013 0.002 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 2926) covalent geometry : angle 0.68919 ( 3986) hydrogen bonds : bond 0.06167 ( 240) hydrogen bonds : angle 4.47142 ( 714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.083 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.0627 time to fit residues: 3.0715 Evaluate side-chains 36 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.167517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135284 restraints weight = 3032.147| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.78 r_work: 0.3440 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2926 Z= 0.161 Angle : 0.670 9.926 3986 Z= 0.319 Chirality : 0.041 0.139 482 Planarity : 0.005 0.042 490 Dihedral : 4.406 17.064 405 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.68 % Allowed : 12.71 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.43), residues: 383 helix: 1.63 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.14 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.013 0.001 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2926) covalent geometry : angle 0.66966 ( 3986) hydrogen bonds : bond 0.05877 ( 240) hydrogen bonds : angle 4.41565 ( 714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.113 Fit side-chains REVERT: A 431 MET cc_start: 0.7881 (tpp) cc_final: 0.7411 (ttp) outliers start: 8 outliers final: 5 residues processed: 40 average time/residue: 0.0627 time to fit residues: 3.1613 Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.168545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136171 restraints weight = 2976.770| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.80 r_work: 0.3435 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2926 Z= 0.152 Angle : 0.660 9.875 3986 Z= 0.311 Chirality : 0.041 0.137 482 Planarity : 0.005 0.042 490 Dihedral : 4.309 16.356 405 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.34 % Allowed : 15.05 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.43), residues: 383 helix: 1.87 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.06 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.012 0.001 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2926) covalent geometry : angle 0.66040 ( 3986) hydrogen bonds : bond 0.05555 ( 240) hydrogen bonds : angle 4.37061 ( 714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.108 Fit side-chains REVERT: A 431 MET cc_start: 0.7830 (tpp) cc_final: 0.7362 (ttp) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.0570 time to fit residues: 3.0071 Evaluate side-chains 40 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.165945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133169 restraints weight = 3036.896| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.82 r_work: 0.3429 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2926 Z= 0.161 Angle : 0.672 9.864 3986 Z= 0.318 Chirality : 0.041 0.135 482 Planarity : 0.005 0.042 490 Dihedral : 4.326 16.650 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.67 % Allowed : 17.06 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.43), residues: 383 helix: 1.78 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -2.23 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.013 0.001 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 2926) covalent geometry : angle 0.67237 ( 3986) hydrogen bonds : bond 0.05837 ( 240) hydrogen bonds : angle 4.39410 ( 714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.064 Fit side-chains REVERT: A 431 MET cc_start: 0.7804 (tpp) cc_final: 0.7335 (ttp) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.0600 time to fit residues: 3.0801 Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.166633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133633 restraints weight = 2995.746| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.83 r_work: 0.3418 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2926 Z= 0.156 Angle : 0.664 9.827 3986 Z= 0.313 Chirality : 0.041 0.135 482 Planarity : 0.005 0.042 490 Dihedral : 4.321 16.550 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.34 % Allowed : 17.06 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.43), residues: 383 helix: 2.01 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.01 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 471 TYR 0.012 0.001 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2926) covalent geometry : angle 0.66380 ( 3986) hydrogen bonds : bond 0.05678 ( 240) hydrogen bonds : angle 4.37935 ( 714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.063 Fit side-chains REVERT: A 34 ASN cc_start: 0.8187 (m-40) cc_final: 0.7792 (m-40) REVERT: A 166 PHE cc_start: 0.6709 (t80) cc_final: 0.6445 (t80) REVERT: A 431 MET cc_start: 0.7782 (tpp) cc_final: 0.7297 (ttp) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0545 time to fit residues: 2.8401 Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136875 restraints weight = 3034.955| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.86 r_work: 0.3475 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2926 Z= 0.136 Angle : 0.637 9.780 3986 Z= 0.299 Chirality : 0.040 0.136 482 Planarity : 0.005 0.043 490 Dihedral : 4.184 15.197 405 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.67 % Allowed : 18.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.44), residues: 383 helix: 2.32 (0.29), residues: 307 sheet: None (None), residues: 0 loop : -2.01 (0.67), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.010 0.001 TYR A 422 PHE 0.011 0.001 PHE A 348 TRP 0.003 0.000 TRP A 451 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2926) covalent geometry : angle 0.63660 ( 3986) hydrogen bonds : bond 0.04895 ( 240) hydrogen bonds : angle 4.29522 ( 714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.123 Fit side-chains REVERT: A 166 PHE cc_start: 0.6566 (t80) cc_final: 0.6205 (t80) REVERT: A 431 MET cc_start: 0.7686 (tpp) cc_final: 0.7287 (ttp) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.0472 time to fit residues: 2.5888 Evaluate side-chains 39 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 18 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136074 restraints weight = 3063.736| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.87 r_work: 0.3452 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2926 Z= 0.141 Angle : 0.641 9.829 3986 Z= 0.300 Chirality : 0.040 0.133 482 Planarity : 0.005 0.042 490 Dihedral : 4.146 15.251 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.01 % Allowed : 17.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.43), residues: 383 helix: 2.34 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -1.95 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.011 0.001 TYR A 422 PHE 0.011 0.001 PHE A 348 TRP 0.003 0.000 TRP A 451 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2926) covalent geometry : angle 0.64058 ( 3986) hydrogen bonds : bond 0.05125 ( 240) hydrogen bonds : angle 4.28155 ( 714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.121 Fit side-chains REVERT: A 166 PHE cc_start: 0.6582 (t80) cc_final: 0.6250 (t80) REVERT: A 431 MET cc_start: 0.7688 (tpp) cc_final: 0.7311 (ttp) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.0447 time to fit residues: 2.4671 Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 6 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.133912 restraints weight = 3013.040| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.84 r_work: 0.3419 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2926 Z= 0.158 Angle : 0.663 9.874 3986 Z= 0.313 Chirality : 0.041 0.133 482 Planarity : 0.005 0.042 490 Dihedral : 4.218 16.290 405 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.67 % Allowed : 18.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.43), residues: 383 helix: 2.22 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -1.96 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 471 TYR 0.013 0.001 TYR A 422 PHE 0.012 0.001 PHE A 348 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2926) covalent geometry : angle 0.66322 ( 3986) hydrogen bonds : bond 0.05668 ( 240) hydrogen bonds : angle 4.34444 ( 714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.103 Fit side-chains REVERT: A 431 MET cc_start: 0.7751 (tpp) cc_final: 0.7359 (ttp) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.0530 time to fit residues: 2.8209 Evaluate side-chains 41 residues out of total 313 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.166969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133553 restraints weight = 2984.360| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.93 r_work: 0.3427 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2926 Z= 0.147 Angle : 0.649 9.800 3986 Z= 0.306 Chirality : 0.040 0.134 482 Planarity : 0.005 0.042 490 Dihedral : 4.194 15.734 405 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.67 % Allowed : 18.39 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.43), residues: 383 helix: 2.29 (0.29), residues: 308 sheet: None (None), residues: 0 loop : -2.00 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 471 TYR 0.011 0.001 TYR A 422 PHE 0.020 0.001 PHE A 166 TRP 0.003 0.001 TRP A 451 HIS 0.000 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2926) covalent geometry : angle 0.64851 ( 3986) hydrogen bonds : bond 0.05279 ( 240) hydrogen bonds : angle 4.32444 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 986.87 seconds wall clock time: 17 minutes 29.01 seconds (1049.01 seconds total)